On Wed, Feb 4, 2015 at 10:02 PM, 新生大侠 <390155909.qq.com> wrote:
> THank you jason an David, you have do a lot good to my work. I did not
> update the AMBER TOOLs because I am doing the comparing work, In the papers
> I have read, the author used AMBER 10 to do the work. So I have to do just
> like him. I used amber 10 to model the DNA structure, and I have got the
> primary structure successfully. The next work I have to do is doing MD to
> get the equilbrium structure. However, when I wanted to get the prmtop file
> of the DNA using tleap leaprc.ff99sb, something goes wrong: some atoms on
> DNA can not be recognized.
> When I get into the tleap leaprc.ff99sb, the code I have type is" dna1 =
> loadpdb nuc.pdb" , then the pdb was loaded and some atoms were added
> automatically:
> "Created a new atom named: H2' within residue: .R<DA 48>
> Created a new atom named: H2'' within residue: .R<DA 48>
> Created a new atom named: H5' within residue: .R<DA 49>
> Created a new atom named: H5'' within residue: .R<DA 49>
> Created a new atom named: H2' within residue: .R<DA 49>
> Created a new atom named: H2'' within residue: .R<DA 49>
> Created a new atom named: H5' within residue: .R<DT 50>
> Created a new atom named: H5'' within residue: .R<DT 50>
> Created a new atom named: H2' within residue: .R<DT 50>
> Created a new atom named: H2'' within residue: .R<DT 50>
> Created a new atom named: HO3' within residue: .R<DT 50>
> total atoms in file: 1588
> Leap added 206 missing atoms according to residue templates:
> 6 Heavy
> 200 H / lone pairs
> The file contained 204 atoms not in residue templates" (part of the
> report)
> Then, when I want to save the prmtop file, I typed"saveamberparm dna1
> ployAT_vac.prmtop ployAT_vac.inpcrd"
> then the fatal error comes:"Checking Unit.
> WARNING: The unperturbed charge of the unit: -50.000000 is not zero.
> FATAL: Atom .R<DA 1>.A<HO5' 33> does not have a type.
> FATAL: Atom .R<DA 1>.A<H5' 34> does not have a type.
> FATAL: Atom .R<DA 1>.A<H5'' 35> does not have a type.
> FATAL: Atom .R<DA 1>.A<H2' 36> does not have a type.
Look at the library files in $AMBERHOME/dat/leap/lib for nucleic acids.
In particular, I think all_nucleic94.lib is the one that ff99SB loads. The
atom names for all of the atoms in the residues are defined in that file.
You need to make sure the atom names from that library match the atom names
in those residues in the PDB file.
This will be a LOT of changes, and you will almost certainly need to write
a script to do the conversion. It may be unlikely that anybody will have a
script that does this, since it's rare to want to *downgrade* a PDB file
to the old format (far more common to want to *upgrade* them to the new
format).
In general, it would be changes like:
H2' -> H2'1
H2'' -> H2'2
H5' -> H5'1
H5'' -> H5'2
You could also delete all hydrogens from the PDB file and let tleap add
them back (their locations may not be as "good", but it would limit the
changes you need to make to *just* the oxygens).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 04 2015 - 20:30:02 PST
